LDkit: a parallel computing toolkit for linkage disequilibrium analysis

文献类型： 外文期刊

第一作者： Tang, You

作者： Tang, You;Li, Zhuo;Zhou, Yao;Zhou, Yao;Zhou, Yao;Liu, Yuxin;Wang, Aoxue;Wang, Chao;Tang, You;Li, Zhuo;Yu, Helong

作者机构：

关键词： Population genetics; Parallel computing; Graphical user interface; Linkage disequilibrium

期刊名称：BMC BIOINFORMATICS （ 影响因子：3.169； 五年影响因子：3.629 ）

ISSN： 1471-2105

年卷期： 2020 年 21 卷 1 期

页码：

收录情况： SCI

摘要： Background: Linkage disequilibrium (LD) analysis is broadly utilized in genetics to understand the evolutionary and demographic history and helps geneticists identify genes associated with interested inherited traits, such as diseases. There are some tools for linkage disequilibrium analysis either in a local or online way; however, there has been no such tool supporting both graphical user interface (GUI) and parallel computing. Results: We developed a GUI software called LDkit for LD analysis, which supports parallel computing. The LDkit supports both variant call format (VCF) and PLINK 'ped + map' format. At the same time, users could also just analyze a subset of individuals from the whole population. The LDkit reads the data by block and then paralleled the computation process by monitoring the usage of processes. Assessment on the Human 1000 genome data showed that when paralleled with 32 threads, the running time was reduced to less than 6 minutes from similar to 77 minutes using the chromosome 22 dataset with 1,103,547 SNPs and 2504 individuals. Conclusions: The software LDkit can be effectively used to calculate and plot LD decay, LD block, and linkage disequilibrium analysis between a site and a given region. Most importantly, both graphical user interface (GUI) and stand-alone packages are available for users' convenience. LDkit was written in JAVA language under cross-platform support.

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